******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/467/467.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 19553 1.0000 500 20578 1.0000 500 20596 1.0000 500 21208 1.0000 500 21548 1.0000 500 21549 1.0000 500 21685 1.0000 500 22748 1.0000 500 22876 1.0000 500 23272 1.0000 500 23273 1.0000 500 23524 1.0000 500 24002 1.0000 500 24634 1.0000 500 24668 1.0000 500 24926 1.0000 500 24982 1.0000 500 25332 1.0000 500 25512 1.0000 500 25660 1.0000 500 25664 1.0000 500 2612 1.0000 500 261857 1.0000 500 264312 1.0000 500 268213 1.0000 500 269199 1.0000 500 3049 1.0000 500 34560 1.0000 500 38510 1.0000 500 4599 1.0000 500 4676 1.0000 500 5899 1.0000 500 6075 1.0000 500 6638 1.0000 500 8428 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/467/467.seqs.fa -oc motifs/467 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 35 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.231 G 0.239 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.231 G 0.239 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 30 llr = 330 E-value = 2.0e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 112:5511164:421412311 pos.-specific C ::1:3:11::1::11:::11: probability G 8:2a1373614a268:76267 matrix T 196:12:6331:42:622422 bits 2.1 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * * Entropy 1.1 ** * * * (15.9 bits) 0.8 ** * * * * *** * 0.6 ** * * ** * **** * 0.4 ** ******* ******* ** 0.2 ****************** ** 0.0 --------------------- Multilevel GTTGAAGTGAAGAGGTGGTGG consensus CG GTTG TT ATAATT sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38510 43 7.74e-10 ATGGATGGGG GTAGCAGTGAAGAGGTGATGG TTTTGGTTTG 25660 349 9.39e-10 TGCTAACTTT GTTGCTGTGTGGTGGTGGTGG TGGGTGTGTT 25512 99 1.01e-08 TGGCATTGTT GTAGCGGTGTAGTGGAGGGGG TACGTGGTAC 269199 244 1.83e-08 GAGGACTCGC GTTGAGGCGAAGAGGAAGTGG AGGACGGAAG 21549 265 9.42e-08 GCTGGGTGTG GTTGTAGTGAAGGGGTGATCG GATTGGATGG 8428 445 4.44e-07 ATTATTGCTC GTTGCCGGGAGGAGGTGGACT AAGAATTGAA 6638 314 4.96e-07 GCCATTGGAT GTTGAGGAGAAGAAGAGAAGA GAGTTTGTCG 6075 274 7.66e-07 GCCGTTCGTT GTCGCGGGAGGGAGGAGGAGG CTTGTGTAAA 4599 367 7.66e-07 TTCGGTAGGC GTTGAAGTGAGAGGGAAAAGG GGGGGGGAGC 21208 109 7.66e-07 TTCCGAGACT GTTGAGATTTAGGTGTGGTGT TGAGTTCTAT 24982 189 1.05e-06 TGTTTGAGCT GTTGTTGTTTGGTGGTGTCGG TGTGTTGAAG 20596 279 1.16e-06 CGACGGTTAT GTTGAAGTTTGGGAGATGTAG CCCCAATGTT 5899 290 1.29e-06 AAGCTACTGC ATTGAAGTTGGGTTGTGGTGA TACAATACTC 2612 73 1.42e-06 TGTGAATTAG GGAGCAGTGAAGGGGTGGCTG GCTTGGTGGA 23524 91 1.74e-06 CATGTGGTGG ATTGATGGGTGGGCGTGGAGG AGTTTGGTGC 22876 208 2.56e-06 TTCTTCTTCT TTGGCACTGACGAAGAGGTGG CGGGAGAGGG 268213 141 3.09e-06 AGTGGTAATG GTTGGAGGTACGACGAGGATG CCTCAAATCA 23272 250 3.39e-06 ACAAGACGCT GTGGCTGTGAAGAGCAGTGGT TTGCTCCGAG 24668 354 5.33e-06 GATGTAAATA GTTGAGTGTAGGTGGTGGGCT AGATTGGCCG 20578 97 5.33e-06 GATGATGGAT GTGGAGGATAAGAGGTTGATA TGCTCGATGA 24926 147 7.55e-06 ACGCCATGAC GTTGAAATGTGGTTATGTTGA GATCGGACGA 21685 339 1.24e-05 CACTGTGAAT GTTGGAGTGATGTGTTGTTGT CTACATCGTC 21548 108 1.85e-05 TTGTAAGGTC GTTGAGGGAGCGTTGAAGTTG AACTAACCGA 24002 336 2.16e-05 GTGAGTTCTG GAAGAGCTGGAGAGGTTTGGG GAGAGTGCTT 22748 389 2.16e-05 TGCTGCCAAT GTGGAAACGAGGAGGAAGCCT AGTTCGACGA 261857 292 2.33e-05 GCCTGAAGCG TTTGAAGGGAAGAACATGAAG TCAAACTAGT 25664 57 2.70e-05 CTCCGAAGGA GTACCGATGATGATGTGATGG CTCGCATGGC 19553 249 3.62e-05 GGTGATGGGA GTGGCACTTTGGTGATTACGG TGAGTTCTTG 34560 216 4.80e-05 GAAAGAAGCA TACGATGTGAAGTAGAGAATG ACAAGAGCTC 264312 259 8.20e-05 AAGGTTATTG ATCGAAGGTACGTTGTTTGTG TGCTGTTATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38510 7.7e-10 42_[+1]_437 25660 9.4e-10 348_[+1]_131 25512 1e-08 98_[+1]_381 269199 1.8e-08 243_[+1]_236 21549 9.4e-08 264_[+1]_215 8428 4.4e-07 444_[+1]_35 6638 5e-07 313_[+1]_166 6075 7.7e-07 273_[+1]_206 4599 7.7e-07 366_[+1]_113 21208 7.7e-07 108_[+1]_371 24982 1e-06 188_[+1]_291 20596 1.2e-06 278_[+1]_201 5899 1.3e-06 289_[+1]_190 2612 1.4e-06 72_[+1]_407 23524 1.7e-06 90_[+1]_389 22876 2.6e-06 207_[+1]_272 268213 3.1e-06 140_[+1]_339 23272 3.4e-06 249_[+1]_230 24668 5.3e-06 353_[+1]_126 20578 5.3e-06 96_[+1]_383 24926 7.5e-06 146_[+1]_333 21685 1.2e-05 338_[+1]_141 21548 1.8e-05 107_[+1]_372 24002 2.2e-05 335_[+1]_144 22748 2.2e-05 388_[+1]_91 261857 2.3e-05 291_[+1]_188 25664 2.7e-05 56_[+1]_423 19553 3.6e-05 248_[+1]_231 34560 4.8e-05 215_[+1]_264 264312 8.2e-05 258_[+1]_221 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=30 38510 ( 43) GTAGCAGTGAAGAGGTGATGG 1 25660 ( 349) GTTGCTGTGTGGTGGTGGTGG 1 25512 ( 99) GTAGCGGTGTAGTGGAGGGGG 1 269199 ( 244) GTTGAGGCGAAGAGGAAGTGG 1 21549 ( 265) GTTGTAGTGAAGGGGTGATCG 1 8428 ( 445) GTTGCCGGGAGGAGGTGGACT 1 6638 ( 314) GTTGAGGAGAAGAAGAGAAGA 1 6075 ( 274) GTCGCGGGAGGGAGGAGGAGG 1 4599 ( 367) GTTGAAGTGAGAGGGAAAAGG 1 21208 ( 109) GTTGAGATTTAGGTGTGGTGT 1 24982 ( 189) GTTGTTGTTTGGTGGTGTCGG 1 20596 ( 279) GTTGAAGTTTGGGAGATGTAG 1 5899 ( 290) ATTGAAGTTGGGTTGTGGTGA 1 2612 ( 73) GGAGCAGTGAAGGGGTGGCTG 1 23524 ( 91) ATTGATGGGTGGGCGTGGAGG 1 22876 ( 208) TTGGCACTGACGAAGAGGTGG 1 268213 ( 141) GTTGGAGGTACGACGAGGATG 1 23272 ( 250) GTGGCTGTGAAGAGCAGTGGT 1 24668 ( 354) GTTGAGTGTAGGTGGTGGGCT 1 20578 ( 97) GTGGAGGATAAGAGGTTGATA 1 24926 ( 147) GTTGAAATGTGGTTATGTTGA 1 21685 ( 339) GTTGGAGTGATGTGTTGTTGT 1 21548 ( 108) GTTGAGGGAGCGTTGAAGTTG 1 24002 ( 336) GAAGAGCTGGAGAGGTTTGGG 1 22748 ( 389) GTGGAAACGAGGAGGAAGCCT 1 261857 ( 292) TTTGAAGGGAAGAACATGAAG 1 25664 ( 57) GTACCGATGATGATGTGATGG 1 19553 ( 249) GTGGCACTTTGGTGATTACGG 1 34560 ( 216) TACGATGTGAAGTAGAGAATG 1 264312 ( 259) ATCGAAGGTACGTTGTTTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16800 bayes= 9.8019 E= 2.0e-012 -135 -1155 174 -146 -193 -1155 -284 171 -61 -121 -52 105 -1155 -279 201 -1155 106 53 -184 -204 87 -279 48 -72 -93 -121 161 -304 -193 -179 16 113 -193 -1155 140 13 123 -1155 -84 -4 65 -79 74 -204 -293 -1155 201 -1155 77 -1155 -26 42 -61 -179 124 -46 -193 -179 180 -304 77 -1155 -1155 105 -93 -1155 148 -46 -13 -1155 124 -46 23 -79 -52 54 -193 -79 133 -46 -93 -1155 148 -46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 30 E= 2.0e-012 0.100000 0.000000 0.800000 0.100000 0.066667 0.000000 0.033333 0.900000 0.166667 0.100000 0.166667 0.566667 0.000000 0.033333 0.966667 0.000000 0.533333 0.333333 0.066667 0.066667 0.466667 0.033333 0.333333 0.166667 0.133333 0.100000 0.733333 0.033333 0.066667 0.066667 0.266667 0.600000 0.066667 0.000000 0.633333 0.300000 0.600000 0.000000 0.133333 0.266667 0.400000 0.133333 0.400000 0.066667 0.033333 0.000000 0.966667 0.000000 0.433333 0.000000 0.200000 0.366667 0.166667 0.066667 0.566667 0.200000 0.066667 0.066667 0.833333 0.033333 0.433333 0.000000 0.000000 0.566667 0.133333 0.000000 0.666667 0.200000 0.233333 0.000000 0.566667 0.200000 0.300000 0.133333 0.166667 0.400000 0.066667 0.133333 0.600000 0.200000 0.133333 0.000000 0.666667 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GTTG[AC][AG]G[TG][GT][AT][AG]G[ATG][GT]G[TA][GT][GAT][TA][GT][GT] -------------------------------------------------------------------------------- Time 9.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 25 llr = 261 E-value = 1.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 7:a5:7::8452461 pos.-specific C 29:49:582647527 probability G :1:2::2::::12:1 matrix T :::::331::1::21 bits 2.1 1.9 1.7 * 1.5 ** * Relative 1.3 ** * ** Entropy 1.1 *** ** *** * (15.0 bits) 0.8 *** ** *** * 0.6 ****** ******** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel ACAACACCACACCAC consensus C C TT CACAAC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 21548 209 6.19e-08 CGCTACCACA ACAACATCACACCCC CCTAACCTAT 5899 2 1.90e-07 C ACACCACCACCCAAG CCGAGCACGC 38510 448 1.90e-07 AAACAACCGA CCACCACCACACGAC GGACACCGTA 4599 444 2.82e-07 CAAGCTCCCG CCACCACCACAACAC AACCACACTT 19553 62 3.70e-07 AACACCCATG ACAACACCAATCAAC CCCAACGCGG 21549 472 1.09e-06 CGGCCTCGTC ACAGCATCACACCAT TGTCGATAGT 23272 485 1.89e-06 AAGCAGCCAA ACAACACCACTCCAA A 22876 439 2.58e-06 TCCTTGCGAG ACAACAGCACACACA TACCATTTAT 24002 433 2.86e-06 GAGGAAATCT ATACCACCAAACAAC GAGGACACTG 25332 135 3.46e-06 TCTTTGACAG ACAGCTTCAACCCTC ATTGAAGCTG 264312 429 3.81e-06 CTTGCAAATA ACACCAGTAAACGAC GAGAATCATT 261857 394 3.81e-06 GTCTCCCAAT CCAACTCTAACCCAC TTCTTTGTCC 34560 366 4.18e-06 TGACGTTCCA ACGACTTCACACCAC GCCTCGTTCC 24634 326 6.06e-06 GCACCCGACG AGAACAGCAACCACC TCGGCGACGA 23524 469 7.93e-06 ACAAACCCTC CCACCTCCCACCACC CAACGCTCCA 8428 346 8.62e-06 CGCACCAGCA CCAGCAGCACCACTC ATTGCTGAGA 2612 299 1.11e-05 AATGCAACAA ACAACTCGACCAAAC ACCACAACCT 269199 469 1.41e-05 ACCTGTTCCT CCAAGACCACCCCAT ATTCCCTTGT 20578 363 1.41e-05 CAGTGAACCA AGAACAGCAACGCAC ACTTCTCTCT 25512 468 1.66e-05 CCCCTCGGTA ACAGCATCCCAACAT TCATATAACT 4676 282 1.79e-05 GCCTCGTCAA ACAACATCCCAGAAG AACGAAGCAT 23273 468 2.42e-05 GAGCCCTGAC ACACTACCCACCACC CGAGAAACAA 25660 239 2.80e-05 TTGGACAATC ACACATCCACACGTC CTCCTCGCAT 22748 107 4.27e-05 ATTACCTCCT GCACCTTCACCACTC ATTCGGACAC 25664 176 4.57e-05 TTGAGCTTCA ACAACAGTCAACGAG GTCTTAGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21548 6.2e-08 208_[+2]_277 5899 1.9e-07 1_[+2]_484 38510 1.9e-07 447_[+2]_38 4599 2.8e-07 443_[+2]_42 19553 3.7e-07 61_[+2]_424 21549 1.1e-06 471_[+2]_14 23272 1.9e-06 484_[+2]_1 22876 2.6e-06 438_[+2]_47 24002 2.9e-06 432_[+2]_53 25332 3.5e-06 134_[+2]_351 264312 3.8e-06 428_[+2]_57 261857 3.8e-06 393_[+2]_92 34560 4.2e-06 365_[+2]_120 24634 6.1e-06 325_[+2]_160 23524 7.9e-06 468_[+2]_17 8428 8.6e-06 345_[+2]_140 2612 1.1e-05 298_[+2]_187 269199 1.4e-05 468_[+2]_17 20578 1.4e-05 362_[+2]_123 25512 1.7e-05 467_[+2]_18 4676 1.8e-05 281_[+2]_204 23273 2.4e-05 467_[+2]_18 25660 2.8e-05 238_[+2]_247 22748 4.3e-05 106_[+2]_379 25664 4.6e-05 175_[+2]_310 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=25 21548 ( 209) ACAACATCACACCCC 1 5899 ( 2) ACACCACCACCCAAG 1 38510 ( 448) CCACCACCACACGAC 1 4599 ( 444) CCACCACCACAACAC 1 19553 ( 62) ACAACACCAATCAAC 1 21549 ( 472) ACAGCATCACACCAT 1 23272 ( 485) ACAACACCACTCCAA 1 22876 ( 439) ACAACAGCACACACA 1 24002 ( 433) ATACCACCAAACAAC 1 25332 ( 135) ACAGCTTCAACCCTC 1 264312 ( 429) ACACCAGTAAACGAC 1 261857 ( 394) CCAACTCTAACCCAC 1 34560 ( 366) ACGACTTCACACCAC 1 24634 ( 326) AGAACAGCAACCACC 1 23524 ( 469) CCACCTCCCACCACC 1 8428 ( 346) CCAGCAGCACCACTC 1 2612 ( 299) ACAACTCGACCAAAC 1 269199 ( 469) CCAAGACCACCCCAT 1 20578 ( 363) AGAACAGCAACGCAC 1 25512 ( 468) ACAGCATCCCAACAT 1 4676 ( 282) ACAACATCCCAGAAG 1 23273 ( 468) ACACTACCCACCACC 1 25660 ( 239) ACACATCCACACGTC 1 22748 ( 107) GCACCTTCACCACTC 1 25664 ( 176) ACAACAGTCAACGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 17010 bayes= 9.89878 E= 1.4e-006 150 5 -258 -1129 -1129 193 -158 -278 191 -1129 -258 -1129 91 64 -58 -1129 -267 193 -258 -278 150 -1129 -1129 3 -1129 105 0 3 -1129 186 -258 -119 165 -21 -1129 -1129 65 138 -1129 -1129 91 93 -1129 -178 -35 164 -158 -1129 50 105 -58 -1129 133 -21 -1129 -78 -167 156 -100 -119 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 25 E= 1.4e-006 0.720000 0.240000 0.040000 0.000000 0.000000 0.880000 0.080000 0.040000 0.960000 0.000000 0.040000 0.000000 0.480000 0.360000 0.160000 0.000000 0.040000 0.880000 0.040000 0.040000 0.720000 0.000000 0.000000 0.280000 0.000000 0.480000 0.240000 0.280000 0.000000 0.840000 0.040000 0.120000 0.800000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.480000 0.440000 0.000000 0.080000 0.200000 0.720000 0.080000 0.000000 0.360000 0.480000 0.160000 0.000000 0.640000 0.200000 0.000000 0.160000 0.080000 0.680000 0.120000 0.120000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC]CA[AC]C[AT][CTG]C[AC][CA][AC][CA][CA][AC]C -------------------------------------------------------------------------------- Time 18.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 8 llr = 132 E-value = 3.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::11:::1:8:64:84 pos.-specific C a8:98:4938:9:9449:6 probability G :1:1::31:::1:::11:: matrix T :1a:393:839:31:1:3: bits 2.1 * 1.9 * * 1.7 * * 1.5 * ** * * * * Relative 1.3 * **** * *** * * Entropy 1.1 ****** ******** *** (23.8 bits) 0.8 ****** ******** *** 0.6 ****** ******** *** 0.4 ****** ******** *** 0.2 ******************* 0.0 ------------------- Multilevel CCTCCTCCTCTCACAACAC consensus T G CT T CC TA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 25512 445 1.21e-10 TACTACTATC CCTCCTCCTCTCACCCCTC GGTAACAGCA 264312 13 3.01e-10 ACCGCACAGT CCTCCTCCCCTCACAGCAC GACAACCTAC 19553 28 9.17e-09 TTGCCTTGCT CTTGCTTCTCTCACACCAC ACCAAAACAC 20578 314 2.06e-08 TCGTCCGTCG CCTCCTCCTCTCTCCTGAA TATATCTCCT 38510 200 3.50e-08 CTTCTGTCGA CCTCTTTCTTTCTCCACTC CGTAGCCTTG 4599 81 3.74e-08 AACACGGTAG CCTCCTAGCTTCACAACAA ATACTGATAC 3049 14 4.02e-08 GATGAACCCT CGTCTTGCTCTGACACCAA TGCTGGTGGA 34560 465 4.98e-08 GGAAATTTCT CCTCCAGCTCACATAACAC ACGAAACCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25512 1.2e-10 444_[+3]_37 264312 3e-10 12_[+3]_469 19553 9.2e-09 27_[+3]_454 20578 2.1e-08 313_[+3]_168 38510 3.5e-08 199_[+3]_282 4599 3.7e-08 80_[+3]_401 3049 4e-08 13_[+3]_468 34560 5e-08 464_[+3]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=8 25512 ( 445) CCTCCTCCTCTCACCCCTC 1 264312 ( 13) CCTCCTCCCCTCACAGCAC 1 19553 ( 28) CTTGCTTCTCTCACACCAC 1 20578 ( 314) CCTCCTCCTCTCTCCTGAA 1 38510 ( 200) CCTCTTTCTTTCTCCACTC 1 4599 ( 81) CCTCCTAGCTTCACAACAA 1 3049 ( 14) CGTCTTGCTCTGACACCAA 1 34560 ( 465) CCTCCAGCTCACATAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 16870 bayes= 12.3638 E= 3.5e-002 -965 211 -965 -965 -965 170 -94 -113 -965 -965 -965 186 -965 192 -94 -965 -965 170 -965 -14 -103 -965 -965 167 -103 70 6 -14 -965 192 -94 -965 -965 11 -965 145 -965 170 -965 -14 -103 -965 -965 167 -965 192 -94 -965 156 -965 -965 -14 -965 192 -965 -113 129 70 -965 -965 56 70 -94 -113 -965 192 -94 -965 156 -965 -965 -14 56 143 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 8 E= 3.5e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.125000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.750000 0.000000 0.250000 0.125000 0.000000 0.000000 0.875000 0.125000 0.375000 0.250000 0.250000 0.000000 0.875000 0.125000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.125000 0.000000 0.000000 0.875000 0.000000 0.875000 0.125000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.875000 0.000000 0.125000 0.625000 0.375000 0.000000 0.000000 0.375000 0.375000 0.125000 0.125000 0.000000 0.875000 0.125000 0.000000 0.750000 0.000000 0.000000 0.250000 0.375000 0.625000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CCTC[CT]T[CGT]C[TC][CT]TC[AT]C[AC][AC]C[AT][CA] -------------------------------------------------------------------------------- Time 28.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19553 4.63e-09 27_[+3(9.17e-09)]_15_[+2(3.70e-07)]_\ 172_[+1(3.62e-05)]_231 20578 4.80e-08 96_[+1(5.33e-06)]_196_\ [+3(2.06e-08)]_30_[+2(1.41e-05)]_123 20596 5.26e-03 278_[+1(1.16e-06)]_201 21208 4.35e-04 108_[+1(7.66e-07)]_305_\ [+3(6.87e-05)]_47 21548 4.85e-06 107_[+1(1.85e-05)]_80_\ [+2(6.19e-08)]_277 21549 2.66e-06 55_[+1(7.68e-05)]_153_\ [+1(6.73e-05)]_14_[+1(9.42e-08)]_186_[+2(1.09e-06)]_14 21685 2.07e-02 338_[+1(1.24e-05)]_141 22748 5.15e-04 25_[+3(6.01e-05)]_62_[+2(4.27e-05)]_\ 267_[+1(2.16e-05)]_91 22876 2.77e-05 207_[+1(2.56e-06)]_210_\ [+2(2.58e-06)]_47 23272 1.50e-05 249_[+1(3.39e-06)]_214_\ [+2(1.89e-06)]_1 23273 4.84e-02 467_[+2(2.42e-05)]_18 23524 6.37e-05 90_[+1(1.74e-06)]_47_[+1(1.46e-05)]_\ 289_[+2(7.93e-06)]_17 24002 5.54e-04 335_[+1(2.16e-05)]_76_\ [+2(2.86e-06)]_53 24634 5.90e-04 111_[+3(1.10e-05)]_195_\ [+2(6.06e-06)]_160 24668 1.77e-02 353_[+1(5.33e-06)]_126 24926 7.11e-03 146_[+1(7.55e-06)]_333 24982 8.94e-03 32_[+1(5.50e-05)]_92_[+1(9.32e-05)]_\ 22_[+1(1.05e-06)]_291 25332 1.30e-02 134_[+2(3.46e-06)]_216_\ [+2(1.53e-05)]_120 25512 1.37e-12 98_[+1(1.01e-08)]_325_\ [+3(1.21e-10)]_4_[+2(1.66e-05)]_18 25660 3.84e-09 252_[+3(3.80e-06)]_77_\ [+1(9.39e-10)]_131 25664 1.18e-02 56_[+1(2.70e-05)]_98_[+2(4.57e-05)]_\ 310 2612 9.25e-05 72_[+1(1.42e-06)]_205_\ [+2(1.11e-05)]_187 261857 1.21e-03 291_[+1(2.33e-05)]_81_\ [+2(3.81e-06)]_92 264312 3.59e-09 12_[+3(3.01e-10)]_227_\ [+1(8.20e-05)]_149_[+2(3.81e-06)]_57 268213 2.18e-02 140_[+1(3.09e-06)]_339 269199 9.29e-07 243_[+1(1.83e-08)]_204_\ [+2(1.41e-05)]_17 3049 2.85e-04 13_[+3(4.02e-08)]_468 34560 2.60e-07 215_[+1(4.80e-05)]_129_\ [+2(4.18e-06)]_84_[+3(4.98e-08)]_17 38510 3.77e-13 42_[+1(7.74e-10)]_136_\ [+3(3.50e-08)]_229_[+2(1.90e-07)]_38 4599 3.76e-10 80_[+3(3.74e-08)]_267_\ [+1(7.66e-07)]_56_[+2(2.82e-07)]_42 4676 3.99e-02 281_[+2(1.79e-05)]_204 5899 6.55e-07 1_[+2(1.90e-07)]_273_[+1(1.29e-06)]_\ 190 6075 6.25e-03 273_[+1(7.66e-07)]_206 6638 3.74e-03 313_[+1(4.96e-07)]_166 8428 8.31e-05 345_[+2(8.62e-06)]_84_\ [+1(4.44e-07)]_35 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************